Nobody Ever Sees These Things Coming
by Adiji-Sensei
Summary: Voyager has returned home, but it's not going to be the happy homecoming that Kathryn Janeway had in mind. J/C, T/P. M for later chapters.
1. Chapter 1

Disclaimer: I do not own anything to do with Star Trek Voyager.

A/N: Well, this is my first Voyager story, so please don't eat me! Not a lot to say really, except that reviews do mean a lot to me, especially as this is the first one involving Voyager that I have written (I primarily write Naruto and Final Fantasy 7 stories, so feel free to check those out too!). Reviews are very much appreciated, as if I don't get any for a while, I kind of assume that people don't like the story, and stop lol. I am not going to say 'won't update until I get 5 reviews' as that's silly, in my opinion, but I do like to know how I am doing.

Anyway, enough of my rambling! This will be a multi-chaptered story, so there will be more to come!

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Nobody Ever Sees These Things Coming

It felt good to be in the Alpha Quadrant again, but at the same time, it filled the captain of Voyager with a sense of dread. Not everything felt right, things felt different…both on her ship, and in Starfleet. She had heard the rumours from some of her closest friends in Starfleet, but she had not listened. Rumours, that was all they had been, but now that she was back in Federation space, she was beginning to see what some of her dear colleagues had meant.

Kathryn felt like she didn't know some of her crew anymore. Seven had been feeding her every excuse under the sun, as the former Borg did not want to go to Earth for fear of what people would think of her, no matter how many times the captain tried to assure her friend that she would not be judged. However, deep down, she knew that there would be some people who would have a problem with Seven, and the captain felt helpless, but she couldn't do anything about the thoughts of others.

Another problem that the captain had was that the friction between the Maquis crew and the Starfleet crew was making itself known again. The Maquis were worried about what greeting they would receive when they returned to Earth, and a few Starfleet officers wanted them to be placed under arrest when they got back to Starfleet Headquarters.

The closer they got to Starfleet, the larger Kathryn's headache became.

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B'Elanna was nervous to be returning to Starfleet, and not just because she had been so accustomed to living in the Delta Quadrant, but because she was unsure about the futures of her, Chakotay, and the other Maquis members. She had experienced her fair share of fights with members of the official Starfleet crew during the past few months, and she had a feeling that it would be the Maquis against Starfleet when they returned home.

With a sigh, she tapped her commbadge.

"Torres to Chakotay. Could you come to my quarters please?" she asked.

"OK, on my way." Was the response, and the communication link ended. B'Elanna sighed again and walked over to her replicator, getting a coffee for herself. She needed something to try and steady her nerves.

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Kathryn had retired to her ready room, leaving Tuvok in charge. She knew that Chakotay was trying to keep the Maquis members in check, a few of them had started to cause trouble, so she excused him from bridge duty. Now they were back in familiar territory, she felt they didn't need to be as defensive and alert as they had to be in the Delta Quadrant. Just as she was reading one of Tuvok's security reports, her console alerted her to an incoming transmission. It was from Starfleet.

"What can I do for you, Admiral?" she greeted. Her superior just sighed, obviously not in the mood for formalities.

"I understand that you have Maquis members on your ship." He said, and suddenly Kathryn felt like she wasn't going to like where this conversation was going to go. Maybe Chakotay and the other Maquis members were right to be concerned.

"Yes, they have been loyal members of my crew these past few years. Commander Chakotay and the rest of his crew have been of a great help, and are as much a part of my crew as the official Starfleet officers. Why do you bring this up?" she asked, and the Admiral looked down for a moment. By building them up, Kathryn hoped that he would say that the Maquis would be treated as normal, and not as criminals, when they arrived at Starfleet Headquarters.

"They are going to be placed under arrest and tried at Headquarters. I'm sorry, Captain, but they are still criminals, no matter how much they have helped you and your crew. I suggest you inform them. I have other work to attend to, welcome back to the Alpha Quadrant." The Admiral said and ended the transmission.

Kathryn let out a frustrated sigh, she knew the Admiral was a busy man, but she couldn't help but think that he had gone so quickly so that she could not argue. It frustrated her, but there seemed to be little she could do. She only hoped that Chakotay would take the news well. Part of her wanted to tell him now, but the problem with that was, she didn't know how to.

Not only that, but she didn't want to put their relationship in jeopardy.

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Chakotay was finally at B'Elanna's quarters. He had a rough idea of what she wanted to talk to him about, but he did not know about her worries or concerns. It took her seconds to tell him to enter, and what the first officer saw shocked him. His friend had never looked so subdued, or so quiet.

_She must be really worried._ Chakotay thought as he took a seat opposite the half Klingon woman.

"What's going to happen to us, Chakotay?" B'Elanna asked, looking at her tattooed friend with worried eyes. Chakotay sighed, not sure what to tell her. He was just as worried about the Maquis crew members as she was, and he intended to speak with the captain, though he wanted to speak to her anyway about other matters.

"I don't know, but I wish I did. Starfleet may caution us, they may let us go. I have no idea, but I intend to speak to the captain, as she may have heard something from Starfleet Headquarters. As soon as I know something, you will be the first person I come to, so we can tell the rest of the Maquis members on this ship together." He said, and was pleased to see a smile find it's way onto his colleague's face.

"Thank you, Chakotay. That means a lot to me, that you trust me to come to me first." She said, and Chakotay let out a laugh.

"You have been my friend for many years, B'Elanna, of course I can trust you."

Before anything else could be said, Janeway's voice filled the room.

"Janeway to Chakotay, come to my ready room immediately."

"On my way. Perfect timing, I'll make your concerns known, B'Elanna." Chakotay said with a friendly smile. Torres nodded and watched as her comrade left her quarters.

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_I have no idea how I am going to break this news. I don't want to lose you, but I fear I will. I don't want to lose anyone, you and your own crew have been wonderful assets to the overall crew of Voyager. I remember when we finally admitted we had feelings for each other, why does it feel like our time together is being cut short?_

Janeway's inner thoughts were cut off when the door chime sounded and Chakotay walked into the room. The captain gave him a sad smile, then walked over and embraced her lover.

"I'm so sorry."

Those three words filled the man with dread, this wasn't going to be a pleasant chat, he could feel it.

"I take it the Maquis members aren't going to be welcomed with open arms?" he asked when Kathryn let him go.

"They want to arrest every Maquis crewman on this ship, that includes you, B'Elanna, and I imagine Tom as well. The Admiral cut me off before I could argue against it. I told him how I have come to trust and befriend nearly every member of the Maquis on this ship over the years, but he would not listen."

Chakotay sighed and watched as Kathryn turned to look out of the window. This was certainly a mess, and he wasn't sure that Voyager's captain could sort this one out. The first officer was about to respond when Kathryn's console bleeped, telling her a transmission was coming through. There was a fleet ready to greet them, the ships were visible out of the windows now, and the captain's heart filled with dread. Pressing a button on her console, she saw the face of one of the security officers at Headquarters. He looked unfamiliar to her, though she was sure there had been many staff changes at Starfleet while Voyager had been gone.

"Captain Janeway, welcome home. Is it a good time to beam a security team aboard to deal with the Maquis members on your vessel?" he said, obviously not caring for pleasantries. Kathryn sighed and looked at Chakotay briefly. She had never felt so awkward or upset in her life, but she was stuck between a rock and a hard place. Looking back at her screen, she sighed.

"Yes, my chief of security will meet you in Transporter Room One." She said, and ended the transmission.

"So that's it then…well, thank you Captain, but I have to go and speak to the Maquis crewmen." Chakotay said, and began to head towards the doors.

"Chakotay, wait!" Kathryn said and ran to grab her lover's arm, though she was not sure if she could class him as her boyfriend anymore.

"Save it, Kathryn. I have a crew to speak with." He said coldly and shook his arm from her grip before leaving the room.

Janeway had to fight to keep the tears from spilling.

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A/N: Well, my first Voyager fanfic…hope I am doing ok. One of the worst things about starting a new fic is wondering if anyone else has done the idea already lol. Anyway, thanks for reading and please review! Flames will be used to roast marshmallows, but I am open to constructive criticism, as this is my first Voyager fic.


	2. Chapter 2

Disclaimer: Still don't own anything to do with Star Trek Voyager

A/N: Well, no reviews as of yet, but I will submit another chapter. I do like feedback though, as I like to know how I am doing, as without reviews, I won't be able to improve or know if people are enjoying the story. Anyway, another chapter for you, I hope to get them a bit longer as the story goes on. Please read and review!

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Chapter 2:

Kathryn's stomach was filled to capacity with butterflies as she made her way to the transporter room. She had decided to go and greet the security chief, who she had learnt was called Kayato, personally as he would be a guest on her ship. The captain hoped that they would be able to talk before he ordered his security team to seize the Maquis members of the crew. She was going to try and use her diplomacy skills as best as she could, as she genuinely felt that though they were Maquis…hell, some of them had started referring to themselves as ex-Maquis, they were still part of Voyager's crew.

Within minutes, Kayato had materialised in front of her eyes. She tried to look positive and confident, even though she felt sick with anxiety, and hoped the lieutenant would be willing to discuss the situation with her before acting.

"Lieutenant Kayato, welcome to Voyager." She said with a smile and held out her hand for him to shake. He accepted, and looked around the transporter room, before focusing his attention back on Kathryn.

The captain had decided to look up the security chief's personal record while she awaited his arrival. He had an impressive file, and from what she had read, he was one of the highest renowned security officers at Starfleet Headquarters.

Kayato continued to observe the room, clearly impressed with what he saw. Kayato was of Japanese descent, and had joined Starfleet against the wishes of his parents. He had always had a passion for space, and with the experience of being a bodyguard under his belt, he decided to become a security officer. He looked skinny and small, but he was incredibly nimble, and skilled in many forms of martial arts. This made him a near-perfect candidate to fill the position of security chief.

"If the rest of your ship is as impressive as this, then I look forward to seeing it." He said and let go of Janeway's hand.

_At least he's polite, hopefully he will be this reasonable for his entire stay. I may be able to negotiate with him…well…I hope I can._

Kathryn came out of her thoughts quickly and looked at Kayato. He didn't seem to have noticed that she had blanked out for a moment.

"I have a request, Lieutenant. I understand that Voyager's original mission was to go after the Maquis crew, but they have served me greatly over these past few years, and their insight and ways have proved useful in many of the situations we have encountered. Would I be able to hold a discussion with you in my ready room?" she asked, deciding to get right to the point. It would do her no good to beat around the bush.

Kayato looked over at her, surprise evident on his face. He had not expected her to request something like that, and though it seemed absurd, he was curious as to what she was going to say. Had the Maquis really been helpful, or had they caused nothing but trouble? He did not trust them at all, like the majority of Starfleet personnel, but he decided to put his prejudice aside and listen to what the captain had to say.

"Very well, will it just be us or will there be others present?" the Japanese officer asked.

"It will be myself, as well as Commander Chakotay, who was leading the Maquis crew we were sent after. Also present will be B'Elanna Torres, who was formally chief engineer with the Maquis crew, but now serves as Voyager's chief engineer. My chief of security Tuvok will also be attending, as will the ship's morale officer, Neelix." Kathryn informed him. She did not think there was any point in bringing Harry or Tom into the meeting.

"Forgive me, Captain, but two Maquis in such high ranks? With all due respect, was that really such a wise idea?" Kayato said, not fully believing what he had just heard.

"Commander Chakotay has been a loyal and trusted first officer while we have been lost in the Delta Quadrant, and a loyal friend. The same applies to B'Elanna, her engineering skills have been a valuable addition to this crew, and they have both served this ship to the best of their ability…acting as Starfleet officers. Anyway, I think it is best if we make our way to my ready room, so that we can get this situation resolved as soon as possible. If you would follow me please." Kathryn said, and left the transporter room, with Kayato not too far behind.

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The atmosphere in the mess hall was awful. Neelix had been informed of the meeting with the Japanese security chief, and in some ways he was looking forward to it, but in other's, he was dreading it. Neelix had come to befriend and help members of both crews, and it was hurting him to see them divided once more.

_Sometimes I wish we had never come back to this quadrant. Both crews learnt to work as one, and there was unity nearly all over the ship. Well, Voyager had to return home sometime I suppose…it's just a shame that the crew will be split._

The Telaxian had come to learn who was Maquis and who was Starfleet, and looking out at the tables, he could see how divided the two crews had become. Starfleet personnel were on one side of the room, and Maquis were on the other. It saddened Neelix to know that the unity was falling to pieces and there was nothing he could do about it.

He knew that all he could do was see if the meeting produced any results.

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Chakotay and B'Elanna decided to make their way to the captain's ready room together, for support if nothing else. They walked in tense silence, neither officer sure of what to say, not that they could think of anything to make the situation at least sound better than it really was.

As they walked, a Maquis who had been given the rank of ensign rounded the corner, nearly bumping into the two senior officers.

"Chakotay, what's going to happen? The Captain won't betray us, will she?" The ensign, who's name was Lexie, asked, panic in her voice. She knew that with no other Starfleet officers around, she could be on first-name terms with the two officers in front of her. It had always been that way, and whenever the Maquis got together, it always went back to the old ways.

"I don't know, Lexie. She can only do so much. B'Elanna and I are on our way to a meeting with this…Kayato…don't worry, everything will work out." The first officer said with a smile that he hoped was reassuring.

"And anyway, we have plenty of Maquis tricks that Starfleet don't know about." B'Elanna added with a grin. The half-Klingon knew that her comment had the desired affect as Lexie was now grinning along with her.

"That's true, anyway, I have a few duties to attend to. Excuse me." The ensign said, bowing her head to the pair of them before continuing on her journey. B'Elanna and Chakotay watched her go for a few moments before going their own way. After more silence, B'Elanna turned to her friend.

"Do you think she'll hand us over?" she asked, and Chakotay sighed.

"I have no idea."

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It was a completely different situation on the bridge. Tuvok had left to go into the captain's ready room, leaving Harry to get some command hours in while everything was calm. The ensign looked over at Tom, who had been quiet ever since Kayato had come aboard.

"I wonder what's going to happen with the Maquis." Harry mused out loud, and Tom turned around to look at his friend.

"Probably jail, to be honest. I've heard the captain talking; Starfleet isn't the same place that we left behind all those years ago. Many rumours of corruption…I wouldn't be surprised if they were true, to be honest. Though forgive me for being selfish, but what's going to happen to me? Will I be given a trial, or just sent back to the place I was before?" The pilot said, and Harry sighed. He couldn't blame his friend for being concerned, hell, every member of the crew had their own concerns about the current situation.

He only hoped the meeting produced some positive results.

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"The bottom line is, Captain, these are the criminals that we sent you out to capture. You know how much trouble they were causing with the Cardassians…are you saying we should release them and let them go and cause that same trouble again?" Kayato said, fighting to keep his voice level. If he was to remain diplomatic, he had to keep calm, the Japanese man knew this.

Chakotay and B'Elanna, however, were growing more and more annoyed. The security chief was talking about them like they weren't there, and it was starting to grate on their nerves.

"You are ready to assume that we will continue fighting the Cardassians, why is this? Many things have changed in these past few years with the Maquis. Thanks to the Captain, we were accepted into Starfleet's way of life on this ship, and that will always remain with us. Why do you assume that we will return to our Maquis ways?" Chakotay argued, fighting to keep his voice level.

"Once a Maquis, always a Maquis." Kayato said, looking straight into the first officer's eyes, almost daring him to argue further.

Kathryn felt like she was fighting a losing battle. Kayato had a point, Voyager's original mission was to intercept the Maquis and take them into custody, but after so many years, did that mission still stand? Many things had changed, the Maquis being one of them. She didn't know what else she could do.

The captain was snapped away from her thoughts but Tuvok's voice.

"I am afraid to say that the security chief has a point. That was our original mission, and the purpose of me infiltrating the Maquis crew in the first place. We were given no instruction to abort the mission, so technically, the mission still stands." The Vulcan stated in his normal, calm tone. That was enough for B'Elanna, she didn't want to hear anymore. However, before she could speak, Kathryn turned to her, regret written all over her face.

"I'm sorry, B'Elanna…Chakotay…gather the Maquis together…you will all have to go with Lieutenant Kayato."

That was the breaking point. B'Elanna shot up out of her seat, sending it flying backwards.

"How could you?! After all our crew has done to help you! I thought we were your friends, Janeway, I thought that we were allies! It seems that we were all wrong to trust you! May you, your ship, and Starfleet rot and die!" she shouted and stormed out of the ready room. Neelix, who had been silent all meeting, ran after her, but not before rounding on Kayato.

"Look what you've done! It is your fault that this crew has fallen apart! I hope you're happy!"

Kathryn watched the pair go, and felt the tears sting her eyes, but she couldn't let them fall, not yet.

"Lieutenant, may I suggest going to the mess hall to relax for a while. I have some things I need to sort out." She said, and Kayato knew that he was not welcome there at the moment, so did as she asked. Tuvok also took that opportunity to leave.

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Tom had seen B'Elanna flee from the room and head for the turbolift, with Neelix in hot pursuit. He looked over at Harry, who nodded, signalling that Tom could follow his wife and the morale officer.

Once they were in the turbolift, the engineer broke down. She began to sob into Tom's shoulder. B'Elanna knew that they could potentially be apart for a long time, depending on what happened in the trial.

_Me, Chakotay, and the rest of the Maquis may even end up on the run. If that happens, I don't know if I'll ever see you again, Tom._

Paris just let her cry, he knew they would have plenty of time to talk later. He knew how upset she was, as his wife very rarely shed a tear. This was serious, and he was content to stay quiet until she wanted to talk.

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The air grew thick as the tension mounted in the ready room. Kathryn couldn't take it any more, and turned to glare at Chakotay.

"So are we just going to stand here glaring at each other or are we going to talk?" she said, trying to keep her voice calm.

"I don't think you have any right to be getting irate, Kathryn. You've just pretty much sentenced me and my crew to a life in jail. Thank you very bloody much, I hope you're pleased with yourself." The tattooed man replied, also fighting to keep calm. Very rarely did he lose his temper, and the last thing he wanted to do was start shouting. Hell, that would probably make everything worse.

"I have no choice, Chakotay! I have to let Kayato take you! Do you think this is easy on me? I can tell you that it isn't. We've been through so much together, hell, all of us have. We are one big family, and me and you, we're the leaders of that family. Please, I never wanted this to happen. I love you, and it hurts that you, B'Elanna, and the rest of your crew have to leave. Where is this going to leave us?" Kathryn said, having a rare moment of emotional weakness. Another thing that shocked her was how easily they were talking as if their crews were separate, the same way they spoke the day they met.

"There is no 'us' anymore, Kathryn. What happened to your fighting spirit? You can stare down the Borg, yet you can't stand up for what's right? You obviously hold little regard for all that we have been through. Both crews united, which I thought would never happen, and now you are throwing that away. I hope you're pleased with yourself Kathryn…but don't feel too bad, you know me and my crew will be fighting Cardassians again in no time. There are plenty of Maquis secrets you don't know about." He told her, moving towards the door.

"Chakotay…you don't mean that…" the captain said, voice faltering. She couldn't believe that there was any truth to the words her lover had just spoken.

"I mean every word, Kathryn. If we do happen to meet again some time in the future, don't think for one minute you'll be getting any help from the Maquis. As B'Elanna said, Voyager can rot and die. I just feel sorry for the poor souls who have to go down with you." Chakotay said and left the room before Kathryn could say anything more.

All she could do was watch him go.

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A/N: Well, that's another chapter. The next one will be the trial. Thanks for reading and please review!


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